+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10572 | ||||||||||||||||||||||||
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Title | Baseplate of native GTA particle, asymmetric reconstruction | ||||||||||||||||||||||||
Map data | baseplate of native GTA particle, asymmetric reconstruction | ||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Tip attachment protein J ...Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Tip attachment protein J / Putative phage tail protein / Glycoside hydrolase superfamily Similarity search - Domain/homology | ||||||||||||||||||||||||
Biological species | Rhodobacter capsulatus DE442 (bacteria) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.56 Å | ||||||||||||||||||||||||
Authors | Bardy P / Fuzik T / Hrebik D / Pantucek R / Beatty JT / Plevka P | ||||||||||||||||||||||||
Funding support | Czech Republic, 7 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure and mechanism of DNA delivery of a gene transfer agent. Authors: Pavol Bárdy / Tibor Füzik / Dominik Hrebík / Roman Pantůček / J Thomas Beatty / Pavel Plevka / Abstract: Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the ...Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10572.map.gz | 12.9 MB | EMDB map data format | |
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Header (meta data) | emd-10572-v30.xml emd-10572.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10572_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_10572.png | 125.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10572 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10572 | HTTPS FTP |
-Validation report
Summary document | emd_10572_validation.pdf.gz | 262.5 KB | Display | EMDB validaton report |
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Full document | emd_10572_full_validation.pdf.gz | 261.6 KB | Display | |
Data in XML | emd_10572_validation.xml.gz | 11.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10572 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10572 | HTTPS FTP |
-Related structure data
Related structure data | 6tb9C 6tbaC 6te8C 6te9C 6teaC 6tebC 6tehC 6to8C 6toaC 6tsuC 6tsvC 6tswC 6tuiC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10572.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | baseplate of native GTA particle, asymmetric reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rhodobacter capsulatus DE442 gene transfer agent baseplate
Entire | Name: Rhodobacter capsulatus DE442 gene transfer agent baseplate |
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Components |
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-Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent baseplate
Supramolecule | Name: Rhodobacter capsulatus DE442 gene transfer agent baseplate type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: host recognition device present at the tip of the tail |
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Source (natural) | Organism: Rhodobacter capsulatus DE442 (bacteria) |
Molecular weight | Theoretical: 1.00 MDa |
-Macromolecule #1: Putative gene transfer agent protein
Macromolecule | Name: Putative gene transfer agent protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: MAYPESLKAH LQGGVTTLAR AWALARADGR VLGFTDHDVV LRFDGISFEP GSGMTAKAVL QGTGLSVDNT ESYGALSSEA ITEADLLAG RYDGAAVTVW LVNWADPAMR AVIFRGHLGE VSRGAGAFTA ELRGLTAALG QEQGRIYHPR CAAVLGDGRC R FDLTKDGY ...String: MAYPESLKAH LQGGVTTLAR AWALARADGR VLGFTDHDVV LRFDGISFEP GSGMTAKAVL QGTGLSVDNT ESYGALSSEA ITEADLLAG RYDGAAVTVW LVNWADPAMR AVIFRGHLGE VSRGAGAFTA ELRGLTAALG QEQGRIYHPR CAAVLGDGRC R FDLTKDGY ALEAALGGVD EAVVLRLAEG AGFEDRWFEK GRLVVLDGAA AGLIGVVKND RLQADGSRLI ELWQRLGANP VA GDRVRIE PGCDKRAGTC RLKFDNFLNF RGFPHIPGED WMVSYPVQSG TNDGGSLFR |
-Macromolecule #2: Putative gene transfer agent protein
Macromolecule | Name: Putative gene transfer agent protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Sequence | String: MATILLSAAG AAIGGGFGGT VLGLSGAVIG RAVGATLGRV IDQRLLGSGS QSVETGRVDR LRLSSASEGE AVGRLWGRMR VAGQVIWAT RFFESASVEK SGKGVPRATV TSYSYSLSLA LALCEGEILR VGRVWADGSE IEVSGLNMRV YRGGEDQLPD P KIAAVEGA ...String: MATILLSAAG AAIGGGFGGT VLGLSGAVIG RAVGATLGRV IDQRLLGSGS QSVETGRVDR LRLSSASEGE AVGRLWGRMR VAGQVIWAT RFFESASVEK SGKGVPRATV TSYSYSLSLA LALCEGEILR VGRVWADGSE IEVSGLNMRV YRGGEDQLPD P KIAAVEGA EAAPAYRGIA YVVLEDLQLA PFGNRVPQFT FEVVRAAQGA LAEAEPDLTR GLRAVALIPG TGEYALATTP VY LATGSGV TATQGVANQN APGGQTDLVA ALERLDEELP NCGAVSLVVS WFGDDLRCGA CDVKPKVASV AEEGANMPWR VAG LERAGA EEVPRLSGQS VYGGTPADAA VIEAIAALRA AGKAVTFYPF ILMAQLAGNG LPDPWNPGSA QPALPWRGRI TLSV APGRA GSPDGTAAAE AQVAGFFGAA SPGDSAIAGG EVVYSGPEEW SMRRFILHYA HLCQLAGGVD AFCIGTEMVA LTQIR GPSN SFPAVAAFRQ LAGEVKAILG PGCKIGYAAD WSEYWGYAPG NGERFFHLDP LWADENIDFI GIDNYLPLSD WRDGAD HAD AGWGSIHALD YLRSNIEGGE YYDWFYAAPE HRAAQIRTPI TDGDHDEPWI WRAKDLRNWW LNDHHERVGG LRSEVAT AW VPQSKPIWFT EMGCAAIDKG TNQPNKFLDP KSSESGLPHH SDGRRDELIQ MQYLRAMTGY WGEAARNPVS AVYGGPML D MSRAHVWAWD ARPWPQFPLN TALWSDGENY ARGHWISGRA VAQPLASVVA EICGAAGITE IDVSGLYGLV RGYTMTGDQ TGRAGLQALM LAYGFEALER DGQLVFRMRD GRVAADLAAA DLALGEGEAV VETVRAAEAE IAGRVRLAYV EAEGDFEVKA VEAVFPDAA AGAAAGSELS LALTRAQAQG IVGRWLAEAR VARDTARFAL PPSRGHLGTG DVVRLDLPEG KRRYRIDRVE Q AGLIQVEA VRVEPGIYAP ADEVEDPASL RPFAAPVPVT AVFLDLPLMK GDEDPVAPHL AVTATPWPGT VAVWSSDEDA GY ALNASLG TRAVIGQTLT PLFRARPGVW DRGAALRVRL ASGALDSATA AKVLNGANAM AIGDGSSENW EVFQFAEAAL VEG KIWDIS LRLRGQLGTD ALMPEVWPEG SVVVALNGAP EQILLPSAAR GLARHYRIGA AVRSYDDPSF VHRIEAFAGA GLRP FSPCH LRAEPGASGW AFRWVRRTRI DGDSWQGYEV PLGETAELYL VRVLEGTAVK REVTVGEASW SYPAALQAAD GIAGA FTLE VAQVSDVYGP GLAARITVGA |
-Macromolecule #3: Putative gene transfer agent protein
Macromolecule | Name: Putative gene transfer agent protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Sequence | String: MAFHEVRFPA NLSFGSVGGP ERRTEIVTLS SGHEERNSPW AHSRRHYDAG VGLRSLDDVE RLIAFFEARG GQLHGFRWKD WADFKSCPA SRAVAHEDQL IGMGDGVTTA FQLVKTYVSG GQSYLRPIVK PVEGTVKLGI AGDHQAEAVN FAVDHATGIV S FNEPPPQG ...String: MAFHEVRFPA NLSFGSVGGP ERRTEIVTLS SGHEERNSPW AHSRRHYDAG VGLRSLDDVE RLIAFFEARG GQLHGFRWKD WADFKSCPA SRAVAHEDQL IGMGDGVTTA FQLVKTYVSG GQSYLRPIVK PVEGTVKLGI AGDHQAEAVN FAVDHATGIV S FNEPPPQG ARVTAGFEFD VPVRFDTDRI AVSVQSFQAG DLPQVPVVEV RI |
-Macromolecule #4: Tail fiber protein Rcc00171
Macromolecule | Name: Tail fiber protein Rcc00171 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Sequence | String: MADQTPLLGL PLILPSQAQK HVTHNEALSL LDAIVQLAVL DRVRTAPPAS PQTGDRHIVA PGGAAAWTGQ DGAVALWTGS GWLFAQPQPG WTARDLSDGA LLIFDGSLWG PAPVATDNLP GLGINTTHDT TNRLAVQAAA TLLSHAGAGH QLKINKALPT DTASLLFQTS ...String: MADQTPLLGL PLILPSQAQK HVTHNEALSL LDAIVQLAVL DRVRTAPPAS PQTGDRHIVA PGGAAAWTGQ DGAVALWTGS GWLFAQPQPG WTARDLSDGA LLIFDGSLWG PAPVATDNLP GLGINTTHDT TNRLAVQAAA TLLSHAGAGH QLKINKALPT DTASLLFQTS WSGRAEMGTT GSDSFAIKVS ADGTAWKTAF SFAGATGLAS GLAVQQSRTD VTAGRLMRAD WGYGPGNLLG TVAQSAGVPT GAVLERGTTA NGEYIRFADG TQICFAQRPL GSIIAQGAGS FAAPYRTADV SWTYPKVFSA APVVTCRGVA PVGLTQDRRL CAGGVGDLDA TAATGIHVVR LGGAANADVF KADLIAIGPW V |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 20 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.8 Component:
Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2 | ||||||||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3114 / Average exposure time: 1.0 sec. / Average electron dose: 42.75 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |